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- PDB-6yn7: Crystal Structure of AHE enzyme from Alicyclobacillus herbarius -

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Basic information

Entry
Database: PDB / ID: 6yn7
TitleCrystal Structure of AHE enzyme from Alicyclobacillus herbarius
ComponentsAHE, beta-glucosidase enzyme
KeywordsHYDROLASE / AHE / Alicyclobacillus herbarius / beta-glucosidase
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesAlicyclobacillus herbarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsGourlay, L.J. / Di Pisa, F.
CitationJournal: Chembiochem / Year: 2021
Title: Release of Soybean Isoflavones by Using a beta-Glucosidase from Alicyclobacillus herbarius.
Authors: Delgado, L. / Heckmann, C.M. / Di Pisa, F. / Gourlay, L. / Paradisi, F.
History
DepositionApr 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AHE, beta-glucosidase enzyme
B: AHE, beta-glucosidase enzyme
C: AHE, beta-glucosidase enzyme
D: AHE, beta-glucosidase enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,54335
Polymers206,4054
Non-polymers2,13831
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint93 kcal/mol
Surface area62570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.045, 93.350, 106.383
Angle α, β, γ (deg.)90.000, 98.692, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
AHE, beta-glucosidase enzyme


Mass: 51601.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus herbarius (bacteria) / Production host: Escherichia coli (E. coli) / References: beta-galactosidase

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Non-polymers , 5 types, 304 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaBr, 20% w/v PEG 3350 0.1 M BT Propane, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.976→105.161 Å / Num. obs: 58817 / % possible obs: 93.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.88 Å2 / CC1/2: 0.996 / Net I/σ(I): 7
Reflection shellResolution: 1.976→2.267 Å / Num. unique obs: 2941 / CC1/2: 0.693

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PTV

4ptv


Resolution: 1.98→98.9 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.3199
RfactorNum. reflection% reflection
Rfree0.2979 1993 3.4 %
Rwork0.247 --
obs0.2488 58600 93.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.62 Å2
Refinement stepCycle: LAST / Resolution: 1.98→98.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14221 0 133 273 14627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001914797
X-RAY DIFFRACTIONf_angle_d0.455920059
X-RAY DIFFRACTIONf_chiral_restr0.03952015
X-RAY DIFFRACTIONf_plane_restr0.00342632
X-RAY DIFFRACTIONf_dihedral_angle_d3.77339873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.297360.39157X-RAY DIFFRACTION1.72
2.03-2.080.4726140.3829415X-RAY DIFFRACTION4.51
2.08-2.140.4007280.3432699X-RAY DIFFRACTION7.61
2.14-2.210.3667350.32971092X-RAY DIFFRACTION11.72
2.21-2.290.3729380.3377969X-RAY DIFFRACTION10.56
2.29-2.380.3453800.32382309X-RAY DIFFRACTION24.76
2.38-2.490.34941100.3173188X-RAY DIFFRACTION34.02
2.49-2.620.36661310.31253945X-RAY DIFFRACTION42.33
2.62-2.790.33261680.30334787X-RAY DIFFRACTION51.39
2.79-30.32162050.28515616X-RAY DIFFRACTION60.25
3-3.30.3292290.27156698X-RAY DIFFRACTION71.5
3.3-3.780.32372920.22598031X-RAY DIFFRACTION86.07
3.78-4.760.24643270.20189318X-RAY DIFFRACTION99.09

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